Evolutionary History of the Human Genome

Abstract

The compositional evolution of the vertebrate genome, from fishes to humans, is of very general interest because of its bearing on the role of natural selection in the evolutionary process.

Keywords: natural selection; isochores; neutral theory; compositional genomics

Figure 1.

(a) Compositional pattern of vertebrate genomes. Histograms showing the relative amounts, modal buoyant densities and modal GC levels of the major DNA components (the families of DNA fragments derived from different isochore families) from Xenopus and human, as estimated after fractionation of DNA by preparative density gradient in the presence of a sequence‐specific DNA ligand (Ag+ or bis(acetatomercurimethyl)dioxane, BAMD). Satellite and minor DNA components (such as ribosomal DNA) are not shown. (b) Compositional patterns of coding sequences represented by GC3 values from Xenopus and human. The broken line at 60% GC3 is shown as a reference. Modified from Bernardi G (1995) The human genome: organization and evolutionary history. Annual Reviews of Genetics29: 445–476.

Figure 2.

The maximum likelihood phylogeny of combined sequences from 11 proteins, 1943 amino acids (from Hedges SB and Poling LL (1999) A molecular phylogeny of reptiles. Science283: 998–1001), is compared with the CsCl profiles (from Thiery JP, Macaya G and Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. Journal of Molecular Biology108: 219–235). Red frames concern warm‐blooded vertebrates (birds, primates), orange and blue frames cold‐blooded vertebrates (reptiles showing a different degree of compositional heterogeneity). The scale bar indicates amino acid substitutions per site. From Cruveiller S, D'Onofrio G and Bernardi G (2000) The compositional transition between the genomes of cold‐ and warm‐blooded vertebrates: codon frequencies in orthologous genes. Gene261: 71–83.

Figure 3.

Scheme of the compositional evolution of vertebrate genomes. At the transition from cold‐ to warm‐blooded vertebrates, the gene‐dense, moderately GC‐rich ancestral genome core (pink box) became the gene‐dense, GC‐rich genome core (red box), whereas the GC‐poor and gene‐poor (blue box) genome desert did not undergo any major compositional change. This transitional (or shifting) mode, which was accompanied by an overall decrease of CpG doublets and mC (methylcytosine), was followed by a conservative mode of genome evolution in which compositional patterns were maintained. Reproduced from Bernardi G (2007) The neo‐selectionist theory of genome evolution. Proceedings of the National Academy of Sciences of the USA104: 8385–8390.

Figure 4.

An example of isochore conservation between syntenic chromosome regions of dog and human. Reproduced from Bernardi G (2007) The neo‐selectionist theory of genome evolution. Proceedings of the National Academy of Sciences of the USA104: 8385–8390.

close

Further Reading

Bernardi G (1995) The human genome: organization and evolutionary history. Annual Reviews of Genetics 29: 445–476.

Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241: 3–17.

Bernardi G (2000) The compositional evolution of vertebrate genomes. Gene 259: 31–43.

Bernardi G (2004, reprinted in 2005) Structural and Evolutionary Genomics. Natural Selection in Genome Evolution. Amsterdam: Elsevier.

Bernardi G (2007) The neo‐selectionist theory of genome evolution. Proceedings of the National Academy of Sciences of the USA 104: 8385–8390.

Carroll RL (1997) Patterns and Processes of Vertebrate Evolution. Cambridge: Cambridge University Press.

Cruveiller S, D'Onofrio G and Bernardi G (2000) The compositional transition between the genomes of cold‐ and warm‐blooded vertebrates: codon frequencies in orthologous genes. Gene 261: 71–83.

Graur D and Li WH (1999) Fundamentals of Molecular Evolution, 2nd edn. Sunderland, MA: Sinauer Associates.

Hedges SB and Poling LL (1999) A molecular phylogeny of reptiles. Science 283: 998–1001.

Saccone S, Federico C, Andreozzi L, D'Antoni S and Bernardi G (2002) Localization of the gene‐richest and the gene‐poorest isochores in the interphase nuclei of mammals and birds. Gene 300: 169–178.

Saccone S, Pavliçek A, Federico C, Paçes J and Bernardi G (2001) Genes, isochores and bands in human chromosomes 21 and 22. Chromosome Research 9: 533–539.

Thiery JP, Macaya G and Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. Journal of Molecular Biology 108: 219–235.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Bernardi, Giorgio(Jul 2008) Evolutionary History of the Human Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005070.pub2]